|
|
Preparation of DNA with local DNA structures
Lofítková, Ellen ; Pernicová, Iva (referee) ; Brázda, Václav (advisor)
In this thesis I focused on quadruplexes and cruciforms formed by DNA. Plasmids pBluescript and others derived from it by inserting oligonucleotid sequences were studied. Sequences forming quadruplexes and cruciforms were found by in silico analysis by QGRS Mapper and Palindrome analyser. Plasmids were transformed into E. coli, isolated and then cleaved with enzymes S1 nuclease and restriction endonuclease ScaI. Cleaving with S1 nuclease predicated presence of local structure. Combined S1/ScaI cleavage did not bring satisfying results due to lost of DNA during purification.
|
|
|
Approximate Palindrome Detection in DNA Sequences
Divila, Jaroslav ; Lexa, Matej (referee) ; Martínek, Tomáš (advisor)
This work deals with conception and implemetation of tools for finding approximate palindromes in DNA sequences. The work focuses on the description of DNA structure, and on the function of palindromes in DNA sequences, and on the description of methods for finding approximate palindromes. Main part of thesis is focused on conclusion and description of implementation approximate palidromes finding tool.
|
|
|
The presence and localization of local DNA structures in the genome of Schizosaccharomyces pombe
Kubínová, Michaela ; Šedrlová, Zuzana (referee) ; Brázda, Václav (advisor)
The thesis focuses on the study of local DNA structures (cruciforms and G quadruplexforming sequence) in the genome of Schizosaccharomyces pombe, a yeast used in the food industry. The analysed local structures are non-randomly distributed within the genome. Based on previous studies, it has been found that they often colocalize with regulatory regions of genes and that the role of these secondary structures in the regulation of basic cellular processes (e.g. replication or transcription) is significant. This analysis was performed using specialized bioinformatics tools (G4Hunter and Palindrome Analyser) that allowed me to identify and analyze these structures in terms of their presence and localization. Many times less IR was found in mtDNA compared to the occurrence of IR in chromosomes. The number and frequency of PQS in mtDNA was also found to be very low. It is very different from the yeast Saccharomyces cerevisiae in this respect. It was also found that the number of IRs found decreases with increasing IR length and about 17% of IRs do not have a loop. A large enrichment of IRs was observed in the repeat_region and rRNA, and in the case of PQS in the rRNA and mRNA regions, i.e. sequences important for cellular processes.
|
|
|
Preparation of DNA with local DNA structures
Lofítková, Ellen ; Pernicová, Iva (referee) ; Brázda, Václav (advisor)
In this thesis I focused on quadruplexes and cruciforms formed by DNA. Plasmids pBluescript and others derived from it by inserting oligonucleotid sequences were studied. Sequences forming quadruplexes and cruciforms were found by in silico analysis by QGRS Mapper and Palindrome analyser. Plasmids were transformed into E. coli, isolated and then cleaved with enzymes S1 nuclease and restriction endonuclease ScaI. Cleaving with S1 nuclease predicated presence of local structure. Combined S1/ScaI cleavage did not bring satisfying results due to lost of DNA during purification.
|
|
|
Approximate Palindrome Detection in DNA Sequences
Divila, Jaroslav ; Lexa, Matej (referee) ; Martínek, Tomáš (advisor)
This work deals with conception and implemetation of tools for finding approximate palindromes in DNA sequences. The work focuses on the description of DNA structure, and on the function of palindromes in DNA sequences, and on the description of methods for finding approximate palindromes. Main part of thesis is focused on conclusion and description of implementation approximate palidromes finding tool.
|
guest ::
